x_vaish kraken v bracken

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        Note that additional data was saved in x_vaish-kraken-v-bracken_multiqc_report_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.21

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        x_vaish kraken v bracken

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-05-29, 13:37 CEST based on data in: /proj/applied_bioinformatics/users/x_vaish/MedBioinfo/analyses/kraken2


        General Statistics

        Showing 16/16 rows and 5/5 columns.
        Sample Name% Corynebacterium kefirresidentii% Top 5 Species% Streptococcus salivarius% Top 5 Species% Unclassified
        ERR6913124
        0.0%
        0.0%
        74.5%
        ERR6913124.brackenreport
        21.6%
        38.8%
        ERR6913139
        1.0%
        14.8%
        23.1%
        ERR6913139.brackenreport
        0.0%
        15.7%
        ERR6913141
        1.6%
        13.2%
        21.7%
        ERR6913141.brackenreport
        0.0%
        5.2%
        ERR6913143
        12.6%
        28.2%
        13.5%
        ERR6913143.brackenreport
        0.0%
        30.8%
        ERR6913220
        0.0%
        0.0%
        9.9%
        ERR6913220.brackenreport
        15.9%
        30.6%
        ERR6913235
        1.4%
        8.2%
        24.0%
        ERR6913235.brackenreport
        0.1%
        12.1%
        ERR6913237
        0.4%
        5.3%
        6.2%
        ERR6913237.brackenreport
        0.0%
        2.4%
        ERR6913239
        6.1%
        17.9%
        11.1%
        ERR6913239.brackenreport
        0.0%
        25.9%

        Bracken

        Bracken is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.DOI: 10.7717/peerj-cs.104.

        Top taxa

        The number of reads falling into the top 5 taxa across different ranks.

        To make this plot, the percentage of each sample assigned to a given taxa is summed across all samples. The counts for these top 5 taxa are then plotted for each of the 9 different taxa ranks. The unclassified count is always shown across all taxa ranks.

        The total number of reads is approximated by dividing the number of unclassified reads by the percentage of the library that they account for. Note that this is only an approximation, and that kraken percentages don't always add to exactly 100%.

        The category "Other" shows the difference between the above total read count and the sum of the read counts in the top 5 taxa shown + unclassified. This should cover all taxa not in the top 5, +/- any rounding errors.

        Note that any taxon that does not exactly fit a taxon rank (eg. - or G2) is ignored.

        Created with MultiQC

        Kraken

        Kraken is a taxonomic classification tool that uses exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.DOI: 10.1186/gb-2014-15-3-r46.

        Top taxa

        The number of reads falling into the top 5 taxa across different ranks.

        To make this plot, the percentage of each sample assigned to a given taxa is summed across all samples. The counts for these top 5 taxa are then plotted for each of the 9 different taxa ranks. The unclassified count is always shown across all taxa ranks.

        The total number of reads is approximated by dividing the number of unclassified reads by the percentage of the library that they account for. Note that this is only an approximation, and that kraken percentages don't always add to exactly 100%.

        The category "Other" shows the difference between the above total read count and the sum of the read counts in the top 5 taxa shown + unclassified. This should cover all taxa not in the top 5, +/- any rounding errors.

        Note that any taxon that does not exactly fit a taxon rank (eg. - or G2) is ignored.

        Created with MultiQC